Intel makes a Matrix RAID manager application that runs from within windows. If you can download it from either Asus or Intel, possibly that utility would be able to "find" the missing drives / RAID 0's?
Be careful I think the Matrix RAID Storage Manager is for up to x58 based motherboards and the newer boards the Rapid Storage Manager is for use, I do not know if they can be used interchangably.
The "chipset RAID limitation" notice is worded incorrectly. It should have meant "you cannot enable RAID without also enabling AHCI", and that setting the chipset's controller to RAID mode will automatically enable AHCI. In other words, any non-RAID disk on a PCH controller set to RAID mode will operate in AHCI mode. If that limitation notice were true, each of the drives on that controller must be RAIDed with another drive in an array - a configuration that would not have supported any optical drives whatsoever. Plus, the Marvell SATA controller does not support optical drives at all - only hard drives. And since at least ICH10R (and probably the ICH9R as well), you can have a non-RAID disk on an ICH/PCH SATA controller set to RAID mode unless that system has a really old Matrix driver version that doesn't support non-RAID disks in RAID mode.
And the second reply is partially correct: The Intel Matrix Storage Controller is usable only up to the ICH10 series SATA controllers. The SATA controller in the LGA 1156 and LGA 1155 chipsets' PCH must use the newer Intel Rapid Storage Technology driver (which is also compatible with earlier Intel SATA controllers).
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The problem is that you installed Windows 7 while the BIOS for the Intel controller was set to AHCI rather than RAID. When you then change from AHCI to RAID Windows won't start since it can't find the correct values in the registry/drivers. I did this too and was quite surprised as I initially thought that RAID was just AHCI with well, just an extra option that sure as heck wouldn't break my Windows installation.
However, this is a solution to this without having to re-install Windows (with the BIOS set to RAID this time). I haven't tried it myself but people in other forums have reported success with this method and you won't screw up anything anyway so it might well be worth a try.
Move your boot HDD from the Intel SATA controller port to a Marvell SATA controller port and make SURE that the Marvell controller is set to AHCI, NOT RAID. Keep the Intel controller in RAID mode. Change the boot order to point to the system disk on the Marvell controller. This way Windows should boot again and you can re-install the Intel Rapid Storage drivers, Windows will discover the Intel RAID controller and add the needed registry changes. Then turn off everything and move the boot HDD back to the Intel controller again. Windows should now load with the Intel controller set to RAID in BIOS.
And RjL, the Marvell controller DOES support optical drives, I'm running my DVD-burner off the Marvell controller on my P67-board without any problems (so far).
I did get the raid working a few days back. Had to install Win7 2 or 3 more times with bios set to RAID first.
Windows decided to put a system reserved partition on one of my raid sets on my second install.
Had to disconnect them and install again on the C: drive ONLY.